Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Methods to Assess Microbial Communities01:19

Methods to Assess Microbial Communities

Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
Synthetic Biology02:55

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
Methods to Assess Microbial Populations01:30

Methods to Assess Microbial Populations

Assessing microbial populations is crucial for understanding microbial roles in health, ecology, and industry. Various complementary techniques—both culture-based and molecular—enable detailed analysis of microbial abundance, diversity, and function.Viable Plate CountThe viable plate count is a traditional culture-based method used to estimate the number of living microbes in a sample. After serial dilution, the sample is spread onto nutrient agar plates. Each viable cell forms a visible...
Key Techniques in Microbiology01:19

Key Techniques in Microbiology

Aseptic techniques prevent contamination, ensure experimental accuracy, and protect researchers and microbial cultures. These techniques are essential in clinical, industrial, and research settings where sterility is required.Maintaining Sterility in Laboratory PracticesScientists maintain sterility by sterilizing tools with heat or chemicals, disinfecting work surfaces, and handling cultures in controlled environments. Working near an open flame or within a laminar flow hood reduces the risk...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Eukaryotic MAGs from the NEREA observatory: expanding the coastal microbiome dataset.

Scientific data·2026
Same author

Persistence of environmental and wastewater-associated antibiotic resistance in river water.

Environmental monitoring and assessment·2026
Same author

Gut microbiome community structure correlates with different behavioral phenotypes in the Belyaev Farm-Fox Experiment.

Communications biology·2026
Same author

Environmental Consequences of Anthropogenic Pollution: Non-antibiotic-Drug-Driven Antibiotic Resistance Selection in a Model Aquatic Ecosystem.

Environment & health (Washington, D.C.)·2026
Same author

Identification of a deep-branching lineage of algae using environmental plastid genomes.

Nature communications·2025
Same author

Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes.

Nature microbiology·2025

Related Experiment Video

Updated: May 10, 2026

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
11:23

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Mastering methodological pitfalls for surviving the metagenomic jungle.

Tom O Delmont1, Pascal Simonet, Timothy M Vogel

  • 1Environmental Microbial Genomics, CNRS, Ecole Centrale de Lyon, Université de Lyon, Ecully, France.

Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology
|June 13, 2013
PubMed
Summary

Metagenomics relies on DNA extraction, sequencing, and bioinformatics. Understanding methodological variations is key to accurate microbial ecology and evolution studies.

Keywords:
biasesdistribution fluctuationmetagenomic

More Related Videos

Metagenomic Analysis of Silage
08:43

Metagenomic Analysis of Silage

Published on: January 13, 2017

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
07:21

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Related Experiment Videos

Last Updated: May 10, 2026

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
11:23

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Metagenomic Analysis of Silage
08:43

Metagenomic Analysis of Silage

Published on: January 13, 2017

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
07:21

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Metagenomics offers a culture- and PCR-independent method for studying microbial evolution, ecology, and biotechnology.
  • Accurate microbial insights depend heavily on DNA extraction, sequencing, and bioinformatics tools.
  • Variations in these methods can significantly impact results across different ecosystems, risking misinterpretation.

Purpose of the Study:

  • To highlight the critical role of methodological choices in metagenomic studies.
  • To emphasize the need for understanding and managing potential pitfalls in metagenomic data analysis.
  • To explore how methodological variations can be leveraged for error analysis in microbial community comparisons.

Main Methods:

  • Review of current metagenomic approaches, including DNA extraction, sequencing technologies, and bioinformatics pipelines.
  • Analysis of how methodological differences influence data interpretation across various ecosystems.
  • Discussion of strategies for evaluating the robustness of metagenomic findings.

Main Results:

  • Methodological variations, particularly in DNA extraction and annotation, can differentially affect results from diverse environments.
  • Lack of complete knowledge of true microbial diversity and proportional representation poses inherent challenges.
  • Variations between different methodological approaches can serve as a basis for assessing the reliability of observations.

Conclusions:

  • Mastering methodological variations is crucial for the validity of metagenomic research.
  • Awareness of potential pitfalls and their ecosystem-specific impacts is essential to avoid ecological misinterpretation.
  • Integrating methodological variations into error analysis can improve the comparison of microbial communities.